Lizard’s Junk DNA is Human Genome’s Treasure

Recently alighted by a post on the Anole Annals that the Anolis genome was taken on by the creationist website Answersingenesis.org, I wondered how the Bible-as-absolute-truth crowd might distort and interpret the meaningful evolutionary insights provided by the lizard genome. The “News to Note” blog written by Dr. Elizabeth Mitchell browses notable science current events featured in mostly secondary media outlets (not the primary literature), providing critiques on conclusions made by researchers that either draw from or provide evidence for evolutionary principles (the entries primarily combat any references to an ancient earth or descent from a common ancestor). Following the link, I was pleased to find that this particular attack on evolutionary research featured a discussion of transposable elements (TEs) in the Anolis genome, the precise focus of my doctoral research!

The blog entry cited a Science Daily article about the release of the Anolis genome in which co-author J. Alföldi was quoted:

“Anoles have a living library of transposable elements,” said Alföldi. The researchers aligned these mobile elements to the human genome, and found that close to 100 of the human genome’s non-coding elements are derived from these jumping genes. “In anoles, these transposons are still hopping around, but evolution has used them for its own purposes, turning them into something functional in humans.”

With a reference to the utility of comparative studies in determining the origins of many aspects of the human genome, Alföldi concludes:

“Sometimes you need to be at a certain distance in order to learn about how the human genome evolved. You have to look out further than you were looking previously.”

Green anole mating (Anolis carolinensis), Caro...

Hey now! Transposable elements active in the green anole have been co-opted by mammalian genomes to provide important functions. Image via Wikipedia

This is certainly true about TEs, because they have been evolving for billions of years and are found in the genomes of all eukaryotes. Vertebrates in particular show a wide range of TE diversity and abundance. In the human genome, as in most mammals, hundreds of thousands of copies of one kind of TE, called L1, dominate the genomic landscape (see the first human genome paper Lander et al. 2001). The Anolis genome contains L1, like human, but also a much wider array of many other kinds of TEs, generally found in relatively low numbers, which is unlike human (reviewed in Tollis and Boissinot 2011).

The interesting aspect of human and lizard TE evolution referred to by Alföldi is that there are some some regions in the human genome that contain parts of TE sequences that are not L1, yet they are highly conserved, meaning that if you were to compare these sequences to their active counterparts in other genomes (like Anolis), they would be almost exactly the same. The last common ancestor of humans and reptiles lived more than 300 million years ago, so one would expect these sequences in their respective genomes would be extremely divergent.

Tuatara

The tuatara is a lepidosaurian reptile that is actually quite different from lizards. If something is found in the genome of the tuatara, green anole, and human, chances are it was present in the common ancestor of all of these species, which lived more than 300 million years ago. Image by SidPix via Flickr

The fact that they are conserved in mammals suggests that purifying selection has been acting on them — their sequence integrity is so important to the function of the host that any DNA mutations would be deleterious and therefore removed by selection. In fact, a paper published in Journal of Heredity (Lowe et al. 2010) showed evidence that one of these elements (also found in the tuatara) regulates the expression of a gene important to embryonic development. The results from the Anolis genome confirm that certain TEs, present in the amniote ancestor, faced starkly different fates as amniotes diversified, maintaining jumping ability throughout reptile evolution while losing it in mammals — where the TE motifs were “domesticated” and utilized by the host to increase its fitness.

This is a fascinating story that highlights the interplay between an organism, its genome, and the selfish genomic parasites which have, in turn, become taken advantage of. It is all made apparent when placed in a comparative — ie, evolutionary context. However, Dr. Mitchell prefers to prune this tree, because she essentially sees all evolutionary explanations as ad hoc at best:

“Any sort of similarity between the lizard and birds or mammals was interpreted as evidence of common ancestry. So was any difference. By assuming that evolution occurred, the researchers simply decorated the evolutionary tree with their data… The interpretation of the data in the shadow of the evolutionary tree of life is unjustified and unproven.”

Finally, she offers her explanation.

“Knowing that God designed all organisms to live in the same world…The fact that some things are similar and others are different does not show that reptiles, mammals, and birds share a common ancestor.”

So, according to creationists, scientists are guilty of making unwarranted assumptions when well-tested hypotheses explain reproducible results. In the meantime, creation-based explanations are completely assumption-free because she just knows that “God designed all organisms”.

Well, if you know, you know.

Can’t really argue with that, I guess.

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2 Comments on “Lizard’s Junk DNA is Human Genome’s Treasure”

  1. […] claim that the anole genome can’t tell us anything about evolution, check out the latest post in Anolis Tollis. GA_googleAddAttr("AdOpt", "1"); GA_googleAddAttr("Origin", "other"); […]

  2. […] Lizard’s Junk DNA is Human Genome’s Treasure […]


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